Organic Molecules

Organic compounds are those that have carbon atoms. In living systems, large organic molecules, called macromolecules, can consist of hundreds or thousands of atoms. Most macromolecules are polymers, molecules that consist of a single unit (monomer) repeated many times

Four of carbon's six electrons are available to form bonds with other atoms. Thus, you will always see four lines connecting a carbon atom to other atoms, each line representing a pair of shared electrons (one electron from carbon and one from another atom). Complex molecules can be formed by stringing carbon atoms together in a straight line or by connecting carbons together to form rings. The presence of nitrogen, oxygen, and other atoms adds variety to these carbon molecules.

Four important classes of organic molecules—carbohydrates, lipids, proteins, and nucleic acids—are discussed in the following sections.

Carbohydrates

Carbohydrates are classified into three groups according to the number of sugar (or saccharide) molecules present:

A monosaccharide is the simplest kind of carbohydrate. It is a single sugar molecule, such as a fructose or glucose (Figure 1). Sugar molecules have the formula (CH2O)n, where n is any number from 3 to 8. For glucose, n is 6, and its formula is C6H12O6. The formula for fructose is also C6H12O6, but as you can see in Figure 1, the placement of the carbon atoms is different. Very small changes in the position of certain atoms, such as those that distinguish glucose and fructose, can dramatically change the chemistry of a molecule.

A disaccharide consists of two linked sugar molecules. Glucose and fructose, for example, link to form sucrose (see Figure 1).

A polysaccharide consists of a series of connected monosaccharides. Thus, a polysaccharide is a polymer because it consists of repeating units of monosaccharide. Starch is a polysaccharide made up of a thousand or more glucose molecules and is used in plants for energy storage. A similar polysaccharide, glycogen, is used in animals for the same purpose.

Figure 1. The molecular structure of several carbohydrates.

Lipids

Lipids are a class of substances that are insoluble in water (and other polar solvents), but are soluble in nonpolar substances (such as ether or chloroform). There are three major groups of lipids:

Triglycerides include fats, oils, and waxes. They consist of three fatty acids bonded to a glycerol molecule (Figure 2). Fatty acids are hydrocarbons (chains of covalently bonded carbons and hydrogens) with a carboxyl group (–COOH) at one end of the chain. A saturated fatty acid has a single covalent bond between each pair of carbon atoms, and each carbon has two hydrogens bonded to it. You can remember this fact by thinking that each carbon is “saturated” with hydrogen. An unsaturated fatty acid occurs when a double covalent bond replaces a single covalent bond and two hydrogen atoms (Figure 2). Polyunsaturated fatty acids have many of these double bonds.

Phospholipids look just like lipids except that one of the fatty acid chains is replaced by a phosphate (–P0 43–) group (Figure 3). Additional chemical groups (indicated by R in Figure 3) are usually attached to the phosphate group. Since the fatty acid “tails” of phospholipids are nonpolar and hydrophobic and the glycerol and phosphate “heads” are polar and hydrophilic, phospholipids are often found oriented in sandwichlike formations with the hydrophobic heads oriented toward the outside. Such formations of phospholipids provide the structural foundation of cell membranes.

Steroidsare characterized by a backbone of four linked carbon rings (Figure 4). Examples of steroids include cholesterol (a component of cell membranes) and certain hormones, including testosterone and estrogen.

Figure 2. The molecular structure of a triglyceride.

Figure 3. The molecular structure of a phospholipid.

Figure 4. Examples of steroids.

Proteins

Proteins represent a class of molecules that have varied functions. Eggs, muscles, antibodies, silk, fingernails, and many hormones are partially or entirely proteins. Although the functions of proteins are diverse, their structures are similar. All proteins are polymers of amino acids; that is, they consist of a chain of amino acids covalently bonded. The bonds between the amino acids are called peptide bonds, and the chain is a polypeptide, or peptide. One protein differs from another by the number and arrangement of the 20 different amino acids. Each amino acid consists of a central carbon bonded to an amine group (–NH 2), a carboxyl group (–COOH), and a hydrogen atom (Figure 5). The fourth bond of the central carbon is shown with the letter R, which indicates an atom or group of atoms that varies from one kind of amino acid to another. For the simplest amino acid, glycine, the R is a hydrogen atom. For serine, R is CH 2OH. For other amino acids, R may contain sulfur (as in cysteine) or a carbon ring (as in phenylalanine).

Figure 5. Examples of amino acids.

There are four levels that describe the structure of a protein:

The primary structure of a protein describes the order of amino acids. Using three letters to represent each amino acid, the primary structure for the protein antidiuretic hormone (ADH) can be written as cys‐tyr‐glu‐asn‐cys‐pro‐arg‐gly.

The secondary structure of a protein is a three‐dimensional shape that results from hydrogen bonding between amino acids. The bonding produces a spiral (alpha helix) or a folded plane that looks much like the pleats on a skirt (beta pleated sheet).

The tertiary structure of a protein includes additional three‐dimensional shaping that results from interaction among R groups. For example, hydrophobic R groups tend to clump toward the inside of the protein, while hydrophilic R groups clump toward the outside of the protein. Additional three‐dimensional shaping occurs when the amino acid cysteine bonds to another cysteine across a disulfide bond. This causes the protein to twist around the bond (Figure 6).

The quaternary structure describes a protein that is assembled from two or more separate peptide chains. The protein hemoglobin, for example, consists of four peptide chains that are held together by hydrogen bonding, interactions among R groups, and disulfide bonds.

Figure 6. Disulfide bonds can dictate a protein's structure.

Nucleic acids

The genetic information of a cell is stored in molecules of deoxyribonucleic acid (DNA). The DNA, in turn, passes its genetic instructions to ribonucleic acid (RNA) for directing various metabolic activities of the cell.

DNA is a polymer of nucleotides (Figure 7 DNA molecule consists of three parts—a nitrogenous base, a five‐carbon sugar called deoxyribose, and a phosphate group. There are four DNA nucleotides, each with one of the four nitrogenous bases (adenine, thymine, cytosine, and guanine). The first letter of each of these four bases is often used to symbolize the respective nucleotide (A for adenine nucleotide, for example).

Figure 7. The molecular structure of nucleotides.

Figure 8 shows how two strands of nucleotides, paired by weak hydrogen bonds between the bases, form a double‐stranded DNA. When bonded in this way, DNA forms a two‐stranded spiral, or double helix. Note that adenine always bonds with thymine and cytosine always bonds with guanine.

RNA differs from DNA in the following ways:

The sugar in the nucleotides that make an RNA molecule is ribose, not deoxyribose as it is in DNA.

The thymine nucleotide does not occur in RNA. It is replaced by uracil. When pairing of bases occurs in RNA, uracil (instead of thymine) pairs with adenine.

RNA is usually single‐stranded and does not form a double helix as does DNA.